Ask for a tools which can mirror a result of FastaAlternateReferenceMaker to an annotation file

Hello. I have identified ~5000 genetic variants including SNPs, indels, and insertions in my yeast strain compared to s288c. Using FastaAlternateReferenceMaker, I made a new consensus sequence by incorporating all variants. Also, I want to change my annotation file as well because the indels and insertions changed the original genome position. Does GATK provide any tools such that I can change my annotation file corresponding to the generated consensus sequence?


  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    HI @YskS

    I just wanted to let you know I am looking into this question.

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin


    Based on your question, the best took I can think of to re-annotate the variants is to rerun the VariantAnnotator.

    But perhaps I am misunderstanding the question. If the VCF is used to generate the fasta, why would the annotations change?

  • YskSYskS Member
    Hi Adelaide,

    Thank you very much.
    I generated the VCF file using Haplotypecaller and used to generate the fasta. However, the VCF file includes insertions, which should shift the position of genes. So, if I use the original annotation file which does not reflect the positional change due to the insertion, I would incorrectly annotate genes. I would like to shift the location of genes in the annotation file (GFF) by reflecting the VCF file information.
  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin


    Apparently, we do not have a tool in GATK directly that does this. However, you might find something in VCFTools That will help you update the annotation.

Sign In or Register to comment.